Spatial Ecology and Macroecology

Practical - Week 2

Florencia Grattarola
grattarola@fzp.czu.cz

MOBI Lab

2024-10-07

What are we going to see today?

How to plot biodiversity data, explore patterns at different resolutions, and make pretty maps.

  1. Create a grid over the study area (extent/grain)
  2. Calculate biodiversity metrics per area (species richness)
  3. Visualisation/mapping (colour schemes)
  4. Description of patterns (hotspots, sampling bias)

Exercises:

  1. GLOBAL scale - expert range maps 🌳 (Europe)
  2. LOCAL scale - occurrence records 🦌 (Czech Republic)

Some preparation before starting to code

Data download

Please download the following files and store them on you data folder:

  • trees.gpkg
  • mammalsCZ.rds
  • CZE_adm0.gpkg
  • KvadratyCR_JTSK.gpkg

Spatial analyses

For geocomputation today we will use the sf package.

library(pacman)
pacman::p_load(sf) # install the package if you haven't already
packageVersion('sf')
[1] '1.0.16'


sf_use_s2(FALSE) # switch spherical geometry off
Spherical geometry (s2) switched off

Spatial data download

For downloading country-specific and world polygons we will use the rnaturalearth package.

pacman::p_load(rnaturalearth, 
               rnaturalearthdata) # the second package is also needed
packageVersion('rnaturalearth')
[1] '1.0.1'

Visualisation

For all the map plots today we will use the ggplot package. It’s part of the tidyverse.

pacman::p_load(tidyverse) # load

GLOBAL Trees of Europe

Mapping species ranges 🌳

Steps:

  1. Get trees’ expert range maps (POLYGONS)
  2. Get a map of Europe
  3. Create a 1-degree grid (POLYGONS)
  4. Calculate species richness per grid cell (SR)
  5. Visualise SR patterns in Europe

Mapping species ranges 🌳

  1. Get trees’ expert range maps

We will get the data from:

Caudullo G., Welk E., San-Miguel-Ayanz J., 2017. Chorological maps for the main European woody species. Data in Brief 12, 662-666. DOI: 10.1016/j.dib.2017.05.007

We will only use the polygon data. See read_tree_data_to_gpkg.R to know how these data were processed.

Mapping species ranges 🌳

  1. Get trees’ expert range maps

Read the data

trees <- st_read('data/trees.gpkg', quiet=T)

Mapping species ranges 🌳

  1. Get trees’ expert range maps

What do the data look like?

trees
Simple feature collection with 81 features and 1 field
Geometry type: MULTIPOLYGON
Dimension:     XY
Bounding box:  xmin: -180 ymin: 20.71311 xmax: 180 ymax: 72.64833
Geodetic CRS:  WGS 84
First 10 features:
           layer_name                           geom
1          Abies_alba MULTIPOLYGON (((16.23493 40...
2  Abies_borisiiregis MULTIPOLYGON (((21.87161 38...
3   Abies_cephalonica MULTIPOLYGON (((22.34088 37...
4      Abies_cilicica MULTIPOLYGON (((36.3169 34....
5   Abies_nebrodensis MULTIPOLYGON (((14.02312 37...
6  Abies_nordmanniana MULTIPOLYGON (((27.08184 39...
7      Abies_numidica MULTIPOLYGON (((5.44332 36....
8       Abies_pinsapo MULTIPOLYGON (((-5.093451 3...
9      Acer_campestre MULTIPOLYGON (((13.77384 37...
10   Acer_platanoides MULTIPOLYGON (((46.89706 43...

Mapping species ranges 🌳

  1. Get a map of Europe

We will download a polygon of the European continent at medium scale, crop it by a defined extent, and finally combine all countries into a unique polygon.

europe <- ne_countries(scale = 50, continent = 'Europe', returnclass='sf') %>% 
  st_crop(., xmin = -30, xmax = 60, ymin = 30, ymax = 73)

europe_union <- st_union(europe) %>% st_make_valid() %>% st_cast() # fixes any problems


Let’s see how it looks

Mapping species ranges 🌳

ggplot() + 
  geom_sf(data=europe_union, fill='white') +
  coord_sf()

Mapping species ranges 🌳

Before working with this map, we need to project the layer.


Earth is not flat :) Projections help us represent the two-dimensional curved surface of the globe into 2D space. There are many ways to do this. Find here a cool Projection Wizard.

Mapping species ranges 🌳

Equal-area maps preserve area measure, generally distorting shapes in order to do that

World Geodetic System (EPSG:4326)

Mollweide (EPSG:19986)

WGS 84 / Equal Earth Greenwich (EPSG:8857)

We will choose ETRS89-extended / LAEA Europe (EPSG:3035), which uses Lambert Azimuthal Equal Area projection.

Mapping species ranges 🌳

Let’s transform the data (both the world and the trees’ layers). We can use the code EPSG:3035.

europe_ea <- st_transform(europe_union, crs = 'EPSG:3035') %>% 
  st_make_valid() %>% st_cast()

trees_ea <- st_transform(trees, crs = 'EPSG:3035') %>% 
  st_make_valid() %>% st_cast()

Mapping species ranges 🌳

  1. Get a map of Europe

Let’s double check that everything is alright

st_crs(europe_ea, parameters = TRUE)$epsg
[1] 3035
st_crs(europe_ea, parameters = TRUE)$ud_unit
1 [m]
st_crs(trees_ea, parameters = TRUE)$epsg
[1] 3035
st_crs(trees_ea, parameters = TRUE)$ud_unit
1 [m]

Mapping species ranges 🌳

  1. Create a global 1-degree grid (POLYGONS)

We will do this using the function st_make_grid()

st_make_grid(
  x,
  cellsize = c(diff(st_bbox(x)[c(1, 3)]), diff(st_bbox(x)[c(2, 4)]))/n,
  offset = st_bbox(x)[c("xmin", "ymin")],
  n = c(10, 10),
  crs = if (missing(x)) NA_crs_ else st_crs(x),
  what = "polygons",
  square = TRUE,
  flat_topped = FALSE
)

Mapping species ranges 🌳

  1. Create a global 1-degree grid (POLYGONS)

For the cellsize argument we will chose 1 degree, which is ~100km (=100,000m)

europe_grid <- st_make_grid(europe_ea, 
                           cellsize=100000,
                           square=FALSE) %>%  # this will make hexagons
  st_intersection(europe_ea) %>% 
  st_sf(gridID=1:length(.))


We have the grid, we are ready to calculate metrics per grid cell. Let’s see how it looks

Mapping species ranges 🌳

  1. Create a global 1-degree grid (POLYGONS)

Mapping species ranges 🌳

  1. Calculate species richness per grid cell (SR)

Let’s plot 5 random species as an example

Mapping species ranges 🌳

  1. Calculate species richness per grid cell (SR)

Now let’s use st_join() to calculate the number of species per grid-cell (SR).

trees_grid <- st_join(europe_grid, trees_ea) %>%
  group_by(gridID) %>%
  summarise(N=sum(!is.na(layer_name)), 
            SR=n_distinct(layer_name, na.rm = TRUE)) %>% 
  st_cast()


This can take a while ☕️🍪

Mapping species ranges 🌳

  1. Calculate species richness per grid cell (SR)

Here are the results :)

trees_grid
Simple feature collection with 1445 features and 3 fields
Geometry type: GEOMETRY
Dimension:     XY
Bounding box:  xmin: 1080899 ymin: 1429727 xmax: 7535328 ymax: 6037921
Projected CRS: ETRS89-extended / LAEA Europe
# A tibble: 1,445 × 4
   gridID     N    SR                                                          .
    <int> <int> <int>                                             <GEOMETRY [m]>
 1      1     0     0                                    POINT (1080899 2579705)
 2      2     0     0 MULTIPOLYGON (((1110023 2538982, 1100617 2543824, 1097498…
 3      3     0     0 POLYGON ((1280899 2362386, 1278435 2364368, 1273591 23748…
 4      4     0     0 POLYGON ((1202323 2535208, 1209886 2532775, 1219309 25259…
 5      5     0     0 POLYGON ((1298076 2253769, 1296932 2252054, 1292751 22550…
 6      6     0     0 POLYGON ((1280899 2381543, 1281344 2381481, 1288628 23688…
 7      7     0     0 POLYGON ((1809887 1531661, 1821808 1530276, 1833394 15180…
 8      8    13    13 POLYGON ((2680899 1833872, 2668639 1826794, 2670835 18324…
 9      9    14    14 POLYGON ((2680899 2007077, 2650401 1989469, 2652179 19948…
10     10    14    14 POLYGON ((2680899 1833872, 2730899 1805004, 2730899 17472…
# ℹ 1,435 more rows

Mapping species ranges 🌳

  1. Visualise SR patterns in the world

Mapping species ranges 🌳

  1. Get trees’ expert range maps (POLYGONS)
  2. Get a map of Europe
  3. Create a 1-degree grid (POLYGONS)
  4. Calculate species richness per grid cell (SR)
  5. Visualise SR patterns in Europe


We are done! No it’s your turn :)

LOCAL Mammal’s of the Czech Republic

Mapping occurrence records 🦌

Steps:

  1. Get occurrence records of mammals in the Czech Republic (POINTS)
  2. Create a grid layer of the Czech Republic (POLYGONS)
  3. Calculate sampling effort (N) and species richness per grid cell (SR)
  4. Visualise N and SR patterns in Czech Republic

You have 30 minutes to work on this. After that, we will code it together :)

Mapping occurrence records 🦌

  1. Get occurrence records of mammals in the Czech Republic

We’ll use the data from last practical (downloaded from GBIF), but his time, we will do a data download using occ_download(). In this way, we can download unlimited records and get a DOI for our dataset (very important for citation).


Check out how it looks like in GBIF, doi: 10.15468/dl.a9fytb.


See download_mammalsCZ_data_from_GBIF.R to see how the data were downloaded.

Mapping occurrence records 🦌

  1. Get occurrence records of mammals in the Czech Republic

Load the data (downloaded from GBIF)

mammalsCZ <- readRDS('data/mammalsCZ.rds')
mammalsCZ
# A tibble: 5,130 × 50
      gbifID datasetKey     occurrenceID kingdom phylum class order family genus
     <int64> <chr>          <chr>        <chr>   <chr>  <chr> <chr> <chr>  <chr>
 1 4.56e-315 6ac3f774-d9fb… ""           Animal… Chord… Mamm… Lago… Lepor… Lepus
 2 4.56e-315 6ac3f774-d9fb… ""           Animal… Chord… Mamm… Prim… Homin… Homo 
 3 4.55e-315 6ac3f774-d9fb… ""           Animal… Chord… Mamm… Arti… Cervi… Cerv…
 4 4.55e-315 6ac3f774-d9fb… ""           Animal… Chord… Mamm… Arti… Cervi… Capr…
 5 4.55e-315 6ac3f774-d9fb… ""           Animal… Chord… Mamm… Arti… Cervi… Capr…
 6 4.55e-315 6ac3f774-d9fb… ""           Animal… Chord… Mamm… Arti… Cervi… Capr…
 7 4.55e-315 6ac3f774-d9fb… ""           Animal… Chord… Mamm… Arti… Cervi… Capr…
 8 4.55e-315 6ac3f774-d9fb… ""           Animal… Chord… Mamm… Arti… Cervi… Capr…
 9 4.54e-315 22a66350-7947… "urn:catalo… Animal… Chord… Mamm… Carn… Muste… Mart…
10 2.45e-314 50c9509d-22c7… "https://ww… Animal… Chord… Mamm… Arti… Suidae Sus  
# ℹ 5,120 more rows
# ℹ 41 more variables: species <chr>, infraspecificEpithet <chr>,
#   taxonRank <chr>, scientificName <chr>, verbatimScientificName <chr>,
#   verbatimScientificNameAuthorship <chr>, countryCode <chr>, locality <chr>,
#   stateProvince <chr>, occurrenceStatus <chr>, individualCount <int>,
#   publishingOrgKey <chr>, decimalLatitude <dbl>, decimalLongitude <dbl>,
#   coordinateUncertaintyInMeters <dbl>, coordinatePrecision <dbl>, …

Mapping occurrence records 🦌

  1. Get occurrence records of mammals in the Czech Republic

Let’s keep only a few fields

mammalsCZ <- mammalsCZ %>% select(species, order, eventDate, 
                                  decimalLongitude, decimalLatitude,
                                  stateProvince, countryCode)

Mapping occurrence records 🦌

  1. Get occurrence records of mammals in the Czech Republic

We will transform our data (table) into an sf object using st_as_sf()

st_as_sf(
  x,
  ...,
  agr = NA_agr_,
  coords,
  wkt,
  dim = "XYZ",
  remove = TRUE,
  na.fail = TRUE,
  sf_column_name = NULL
)

Mapping occurrence records 🦌

  1. Get occurrence records of mammals in the Czech Republic
mammalsCZ %>% 
  st_as_sf(coords=c('decimalLongitude', 'decimalLatitude'),
           crs=4326)
Simple feature collection with 5130 features and 5 fields
Geometry type: POINT
Dimension:     XY
Bounding box:  xmin: 12.203 ymin: 48.63992 xmax: 18.79605 ymax: 50.99892
Geodetic CRS:  WGS 84
# A tibble: 5,130 × 6
   species   order eventDate stateProvince countryCode            geometry
 * <chr>     <chr> <chr>     <chr>         <chr>               <POINT [°]>
 1 Lepus eu… Lago… 2011-06-… ""            CZ           (13.82827 48.8938)
 2 Homo sap… Prim… 2013-12-… ""            CZ          (14.43048 50.09059)
 3 Cervus e… Arti… 2012-12-… ""            CZ          (13.80655 48.82647)
 4 Capreolu… Arti… 2013-10-… ""            CZ          (12.35683 50.13959)
 5 Capreolu… Arti… 2011-06-… ""            CZ           (13.82827 48.8938)
 6 Capreolu… Arti… 2013-06-… ""            CZ          (14.32012 50.09922)
 7 Capreolu… Arti… 2011-06-… ""            CZ          (13.65935 48.99881)
 8 Capreolu… Arti… 2012-12-… ""            CZ          (13.80655 48.82647)
 9 Martes m… Carn… 1961-04-… ""            CZ          (18.28333 49.83333)
10 Sus scro… Arti… 2024-09-… "Středočeský" CZ          (13.84809 50.23607)
# ℹ 5,120 more rows

Mapping occurrence records 🦌

  1. Get occurrence records of mammals in the Czech Republic

And we save

mammalsCZ_sf <- mammalsCZ %>% 
  st_as_sf(coords=c('decimalLongitude', 'decimalLatitude'),
           crs=4326) # this is the projection that the data are in


Note that crs=4326 is related to the EPSG:4326, CRS: WGS 84

Mapping occurrence records 🦌

  1. Create a grid layer of the Czech Republic

First, let’s load the country’s border using st_read

CZ_borders <- st_read('data/CZE_adm0.gpkg', quiet=T)


You can also get country data using rnaturalearth::ne_countries()

Mapping occurrence records 🦌

  1. Create a grid layer of the Czech Republic
CZ_borders
Simple feature collection with 1 feature and 70 fields
Geometry type: MULTIPOLYGON
Dimension:     XY
Bounding box:  xmin: 12.08586 ymin: 48.54084 xmax: 18.86253 ymax: 51.05438
Geodetic CRS:  WGS 84
  GADMID ISO     NAME_ENGLI       NAME_ISO       NAME_FAO      NAME_LOCAL
1     59 CZE Czech Republic CZECH REPUBLIC Czech Republic Ceská republika
       NAME_OBSOL NAME_VARIA NAME_NONLA         NAME_FRENC      NAME_SPANI
1 Moravia|Bohemia      Cesko       <NA> République Tchèque República Checa
  NAME_RUSSI         NAME_ARABI NAME_CHINE      WASPARTOF CONTAINS
1      ????? ????????? ????????      ????? Czechoslovakia     <NA>
       SOVEREIGN ISO2  WWW FIPS ISON  VALIDFR VALIDTO AndyID  POP2000     SQKM
1 Czech Republic   CZ <NA>   EZ  203 19930101 Present     65 10271830 78495.16
   POPSQKM      UNREGION1 UNREGION2 DEVELOPING CIS Transition OECD
1 130.8594 Eastern Europe    Europe          2   0          0    1
               WBREGION            WBINCOME        WBDEBT WBOTHER CEEAC CEMAC
1 Europe & Central Asia Upper middle income Less indebted    <NA>     0     0
  CEPLG COMESA EAC ECOWAS IGAD IOC MRU SACU UEMOA UMA PALOP PARTA CACM EurAsEC
1     0      0   0      0    0   0   0    0     0   0     0     0    0       0
  Agadir SAARC ASEAN NAFTA GCC CSN CARICOM EU CAN ACP Landlocked AOSIS SIDS
1      0     0     0     0   0   0       0  1   0   0          1     0    0
  Islands LDC Shape_Leng Shape_Area                           geom
1       0   0   26.21557   9.813959 MULTIPOLYGON (((13.17648 49...

Mapping occurrence records 🦌

  1. Create a grid layer of the Czech Republic

We will actually load a Czech standard grid layer of 100 km2 area

CZ_grids <- st_read('data/KvadratyCR_JTSK.gpkg', quiet=T)


But you can also create this grid by using st_make_grid() as we did before.

Mapping occurrence records 🦌

  1. Create a grid layer of the Czech Republic
CZ_grids
Simple feature collection with 678 features and 10 fields
Geometry type: POLYGON
Dimension:     XY
Bounding box:  xmin: -912065.7 ymin: -1229672 xmax: -421278.2 ymax: -928997.8
Projected CRS: S-JTSK / Krovak East North
First 10 features:
   OBJECTID ENTITY    AREA PERIMETE KVADRAT         X         Y Shape_Leng
1         1      3 130.032   45.626    4951 -740241.8 -935317.5   45626.41
2         2      5 130.036   45.627    4952 -728665.0 -936923.5   45627.17
3         3      6 130.303   45.675    5051 -741782.9 -946335.6   45675.21
4         4      8 130.040   45.628    4953 -717084.4 -938503.6   45627.96
5         5      9 130.307   45.676    5052 -730181.5 -947945.1   45675.88
6         6     12 130.311   45.677    5053 -718576.3 -949528.8   45676.59
7         7     14 130.050   45.630    4955 -693912.1 -941586.4   45629.61
8         8     17 130.055   45.630    4956 -682320.5 -943089.1   45630.48
9         9     18 130.319   45.678    5055 -695354.9 -952618.5   45678.09
10       10     19 130.060   45.631    4957 -670725.5 -944566.0   45631.36
   Shape_Area   ID                           geom
1   130031546 4951 POLYGON ((-745252.4 -928997...
2   130035855 4952 POLYGON ((-733689.7 -930614...
3   130302745 5051 POLYGON ((-746805.7 -940014...
4   130040349 4953 POLYGON ((-722123.3 -932206...
5   130306551 5052 POLYGON ((-735218.5 -941635...
6   130310574 5053 POLYGON ((-723627.4 -943229...
7   130049749 4955 POLYGON ((-698979.2 -935311...
8   130054715 4956 POLYGON ((-687401.8 -936825...
9   130319128 5055 POLYGON ((-700434.2 -946342...
10  130059749 4957 POLYGON ((-675820.7 -938313...

Mapping occurrence records 🦌

  1. Create a grid layer of the Czech Republic

Check the layer’s Coordinate Reference System (CRS)

st_crs(CZ_borders) == st_crs(CZ_grids)
[1] FALSE

Mapping occurrence records 🦌

  1. Create a grid layer of the Czech Republic

Check the layer’s Coordinate Reference System (CRS)

st_crs(CZ_borders)
Coordinate Reference System:
  User input: WGS 84 
  wkt:
GEOGCRS["WGS 84",
    ENSEMBLE["World Geodetic System 1984 ensemble",
        MEMBER["World Geodetic System 1984 (Transit)"],
        MEMBER["World Geodetic System 1984 (G730)"],
        MEMBER["World Geodetic System 1984 (G873)"],
        MEMBER["World Geodetic System 1984 (G1150)"],
        MEMBER["World Geodetic System 1984 (G1674)"],
        MEMBER["World Geodetic System 1984 (G1762)"],
        MEMBER["World Geodetic System 1984 (G2139)"],
        ELLIPSOID["WGS 84",6378137,298.257223563,
            LENGTHUNIT["metre",1]],
        ENSEMBLEACCURACY[2.0]],
    PRIMEM["Greenwich",0,
        ANGLEUNIT["degree",0.0174532925199433]],
    CS[ellipsoidal,2],
        AXIS["geodetic latitude (Lat)",north,
            ORDER[1],
            ANGLEUNIT["degree",0.0174532925199433]],
        AXIS["geodetic longitude (Lon)",east,
            ORDER[2],
            ANGLEUNIT["degree",0.0174532925199433]],
    USAGE[
        SCOPE["Horizontal component of 3D system."],
        AREA["World."],
        BBOX[-90,-180,90,180]],
    ID["EPSG",4326]]
st_crs(CZ_grids)
Coordinate Reference System:
  User input: S-JTSK / Krovak East North 
  wkt:
PROJCRS["S-JTSK / Krovak East North",
    BASEGEOGCRS["S-JTSK",
        DATUM["System of the Unified Trigonometrical Cadastral Network",
            ELLIPSOID["Bessel 1841",6377397.155,299.1528128,
                LENGTHUNIT["metre",1]]],
        PRIMEM["Greenwich",0,
            ANGLEUNIT["degree",0.0174532925199433]],
        ID["EPSG",4156]],
    CONVERSION["Krovak East North (Greenwich)",
        METHOD["Krovak (North Orientated)",
            ID["EPSG",1041]],
        PARAMETER["Latitude of projection centre",49.5,
            ANGLEUNIT["degree",0.0174532925199433],
            ID["EPSG",8811]],
        PARAMETER["Longitude of origin",24.8333333333333,
            ANGLEUNIT["degree",0.0174532925199433],
            ID["EPSG",8833]],
        PARAMETER["Co-latitude of cone axis",30.2881397527778,
            ANGLEUNIT["degree",0.0174532925199433],
            ID["EPSG",1036]],
        PARAMETER["Latitude of pseudo standard parallel",78.5,
            ANGLEUNIT["degree",0.0174532925199433],
            ID["EPSG",8818]],
        PARAMETER["Scale factor on pseudo standard parallel",0.9999,
            SCALEUNIT["unity",1],
            ID["EPSG",8819]],
        PARAMETER["False easting",0,
            LENGTHUNIT["metre",1],
            ID["EPSG",8806]],
        PARAMETER["False northing",0,
            LENGTHUNIT["metre",1],
            ID["EPSG",8807]]],
    CS[Cartesian,2],
        AXIS["easting (X)",east,
            ORDER[1],
            LENGTHUNIT["metre",1]],
        AXIS["northing (Y)",north,
            ORDER[2],
            LENGTHUNIT["metre",1]],
    USAGE[
        SCOPE["GIS."],
        AREA["Czechia; Slovakia."],
        BBOX[47.73,12.09,51.06,22.56]],
    ID["EPSG",5514]]

Mapping occurrence records 🦌

  1. Calculate sampling effort (N) and species richness per grid cell (SR)

Frist, we will transform the layer’s CRS to S-JTSK / Krovak East North using st_transform().

mammalsCZ_sf <- st_transform(mammalsCZ_sf,  
                             crs = st_crs(CZ_grids)) # the same CRS as the CZ_grids layer

Mapping occurrence records 🦌

  1. Calculate sampling effort (N) and species richness per grid cell (SR)
mammalsCZ_sf
Simple feature collection with 5130 features and 5 fields
Geometry type: POINT
Dimension:     XY
Bounding box:  xmin: -897040.7 ymin: -1224642 xmax: -435147.4 ymax: -943016.8
Projected CRS: S-JTSK / Krovak East North
# A tibble: 5,130 × 6
   species   order eventDate stateProvince countryCode             geometry
 * <chr>     <chr> <chr>     <chr>         <chr>                <POINT [m]>
 1 Lepus eu… Lago… 2011-06-… ""            CZ          (-803959.7 -1168429)
 2 Homo sap… Prim… 2013-12-… ""            CZ          (-742108.4 -1042758)
 3 Cervus e… Arti… 2012-12-… ""            CZ          (-806616.4 -1175608)
 4 Capreolu… Arti… 2013-10-… ""            CZ          (-887913.2 -1015134)
 5 Capreolu… Arti… 2011-06-… ""            CZ          (-803959.7 -1168429)
 6 Capreolu… Arti… 2013-06-… ""            CZ          (-749798.3 -1040726)
 7 Capreolu… Arti… 2011-06-… ""            CZ            (-814507 -1155077)
 8 Capreolu… Arti… 2012-12-… ""            CZ          (-806616.4 -1175608)
 9 Martes m… Carn… 1961-04-… ""            CZ          (-470570.3 -1101814)
10 Sus scro… Arti… 2024-09-… "Středočeský" CZ          (-781040.9 -1020909)
# ℹ 5,120 more rows

Mapping occurrence records 🦌

  1. Calculate sampling effort (N) and species richness per grid cell (SR)

Let’s plot the sf objects

Mapping occurrence records 🦌

ggplot() + 
  geom_sf(data=CZ_borders, fill='white') +
  geom_sf(data=CZ_grids, fill=NA) + 
  geom_sf(data=mammalsCZ_sf)

Mapping occurrence records 🦌

  1. Calculate sampling effort (N) and species richness per grid cell (SR)

To calculate number of records and number of species per grid cell, we will use st_join()

st_join(
  x,    #   object of class sf
  y,    #   object of class sf
  join = st_intersects,
  ...,
  suffix = c(".x", ".y"),
  left = TRUE,
  largest = FALSE
)

Mapping occurrence records 🦌

  1. Calculate sampling effort (N) and species richness per grid cell (SR)

To calculate number of records and number of species per grid cell, we will use st_join()

st_join(CZ_grids,       # POLYGONS (grid cells)
        mammalsCZ_sf)   # POINTS
Simple feature collection with 5341 features and 15 fields
Geometry type: POLYGON
Dimension:     XY
Bounding box:  xmin: -912065.7 ymin: -1229672 xmax: -421278.2 ymax: -928997.8
Projected CRS: S-JTSK / Krovak East North
First 10 features:
    OBJECTID ENTITY    AREA PERIMETE KVADRAT         X         Y Shape_Leng
1          1      3 130.032   45.626    4951 -740241.8 -935317.5   45626.41
2          2      5 130.036   45.627    4952 -728665.0 -936923.5   45627.17
3          3      6 130.303   45.675    5051 -741782.9 -946335.6   45675.21
4          4      8 130.040   45.628    4953 -717084.4 -938503.6   45627.96
5          5      9 130.307   45.676    5052 -730181.5 -947945.1   45675.88
5.1        5      9 130.307   45.676    5052 -730181.5 -947945.1   45675.88
5.2        5      9 130.307   45.676    5052 -730181.5 -947945.1   45675.88
5.3        5      9 130.307   45.676    5052 -730181.5 -947945.1   45675.88
5.4        5      9 130.307   45.676    5052 -730181.5 -947945.1   45675.88
5.5        5      9 130.307   45.676    5052 -730181.5 -947945.1   45675.88
    Shape_Area   ID             species        order  eventDate stateProvince
1    130031546 4951                <NA>         <NA>       <NA>          <NA>
2    130035855 4952                <NA>         <NA>       <NA>          <NA>
3    130302745 5051                <NA>         <NA>       <NA>          <NA>
4    130040349 4953                <NA>         <NA>       <NA>          <NA>
5    130306551 5052     Lepus europaeus   Lagomorpha 2020-06-29  Ústecký kraj
5.1  130306551 5052 Capreolus capreolus Artiodactyla 2020-07-03  Ústecký kraj
5.2  130306551 5052 Capreolus capreolus Artiodactyla 2020-07-09  Ústecký kraj
5.3  130306551 5052 Capreolus capreolus Artiodactyla 2020-06-20  Ústecký kraj
5.4  130306551 5052 Capreolus capreolus Artiodactyla 2020-06-23  Ústecký kraj
5.5  130306551 5052     Lepus europaeus   Lagomorpha 2020-07-13  Ústecký kraj
    countryCode                           geom
1          <NA> POLYGON ((-745252.4 -928997...
2          <NA> POLYGON ((-733689.7 -930614...
3          <NA> POLYGON ((-746805.7 -940014...
4          <NA> POLYGON ((-722123.3 -932206...
5            CZ POLYGON ((-735218.5 -941635...
5.1          CZ POLYGON ((-735218.5 -941635...
5.2          CZ POLYGON ((-735218.5 -941635...
5.3          CZ POLYGON ((-735218.5 -941635...
5.4          CZ POLYGON ((-735218.5 -941635...
5.5          CZ POLYGON ((-735218.5 -941635...

Mapping occurrence records 🦌

  1. Calculate sampling effort (N) and species richness per grid cell (SR)

Now, we need to summarise the data per grid-cell.
Luckily, tidyverse methods also work for sf objects :)


We will do it with group_by() and summarise().

First, we will group by grid-cells and then we count values per grid.

Mapping occurrence records 🦌

  1. Calculate sampling effort (N) and species richness per grid cell (SR)

Let’s calculate the number of records (N) and the number of species per grid-cell (SR)

st_join(CZ_grids, mammalsCZ_sf) %>% 
  group_by(OBJECTID) %>% # the name of the column that has the index
  summarise(N=sum(!is.na(species)), # calculates the number of points in the polygon
            SR=n_distinct(species, na.rm = TRUE))  # calculates the number of different 'species' in the polygon
Simple feature collection with 678 features and 3 fields
Geometry type: POLYGON
Dimension:     XY
Bounding box:  xmin: -912065.7 ymin: -1229672 xmax: -421278.2 ymax: -928997.8
Projected CRS: S-JTSK / Krovak East North
# A tibble: 678 × 4
   OBJECTID     N    SR                                                     geom
      <int> <int> <int>                                            <POLYGON [m]>
 1        1     0     0 ((-745252.4 -928997.8, -733689.7 -930614.9, -733689.7 -…
 2        2     0     0 ((-733689.7 -930614.9, -722123.3 -932206.2, -722123.3 -…
 3        3     0     0 ((-746805.7 -940014.3, -735218.5 -941635, -735218.5 -94…
 4        4     0     0 ((-722123.3 -932206.2, -710553.1 -933771.6, -710553.1 -…
 5        5    27     3 ((-735218.5 -941635, -723627.4 -943229.9, -723627.4 -94…
 6        6     6     3 ((-723627.4 -943229.9, -712032.7 -944798.9, -712032.7 -…
 7        7     0     0 ((-698979.2 -935311.3, -687401.8 -936825.2, -687401.8 -…
 8        8     0     0 ((-687401.8 -936825.2, -675820.7 -938313.3, -675820.7 -…
 9        9     0     0 ((-700434.2 -946342, -688832.2 -947859.3, -688832.2 -94…
10       10     0     0 ((-675820.7 -938313.3, -664236.1 -939775.7, -664236.1 -…
# ℹ 668 more rows

Mapping occurrence records 🦌

  1. Calculate sampling effort (N) and species richness per grid cell (SR)

Let’s store the output into a new object CZ_mammals_grids.

mammalsCZ_grids <- st_join(CZ_grids, mammalsCZ_sf) %>% 
  group_by(OBJECTID) %>% 
  summarise(N=sum(!is.na(species)), 
            SR=n_distinct(species, na.rm = TRUE))

Mapping occurrence records 🦌

  1. Visualise N and SR patterns in Czech Republic

Finally, let’s plot this.
We will do it using geom_sf(), a ggplot function to visualise sf objects

Mapping occurrence records 🦌

  1. Visualise N and SR patterns in Czech Republic
ggplot() + 
  geom_sf(data=mammalsCZ_grids) +
  coord_sf(crs=4326)

Mapping occurrence records 🦌

  1. Visualise N and SR patterns in Czech Republic

Where are the nice colours?

We need to indicate which column from the object should the grids be filled with.

Mapping occurrence records 🦌

ggplot() + 
  geom_sf(data=mammalsCZ_grids, aes(fill=SR)) +
  coord_sf(crs=4326)

Mapping occurrence records 🦌

  1. Visualise N and SR patterns in Czech Republic

Let’s get a nicer color scale.

Bear in mind that we see colors differently. Thus, it’s important to consider colorblind safe palettes

Check out The R Graph Gallery for many cool graphic options with ggplot

Mapping occurrence records 🦌

ggplot() + 
  geom_sf(data=mammalsCZ_grids, aes(fill=SR)) +
  scale_fill_fermenter(palette ='YlOrBr', n.breaks=9, direction = 1) + # fill of the grids
  geom_sf(data=CZ_borders, fill=NA) +
  coord_sf(crs=4326) +
  theme_bw()

Now, here’s a better plot :)

Mapping occurrence records 🦌

  1. Visualise N and SR patterns in Czech Republic

The hotspots of species richness are in cities. How can these be the richest areas for mammals?

Let’s have a look at the sampling effort (N: number of records per grid cell) and compare both layers

Mapping occurrence records 🦌

ggplot() + 
  geom_sf(data=mammalsCZ_grids, aes(fill=N)) +
  scale_fill_fermenter(palette ='YlGnBu', n.breaks=9, direction = 1) +
  geom_sf(data=CZ_borders, fill=NA) +
  coord_sf(crs=4326) +
  theme_bw()

Mapping occurrence records 🦌

What can you say about the hotspots of species richness we found?

Species richness

Number of records

In following steps (e.g., modelling) you should take into account this bias :)

Mapping occurrence records 🦌

  1. Get occurrence records of mammals in the Czech Republic (POINTS)
  2. Create a grid layer of the Czech Republic (POLYGONS)
  3. Calculate sampling effort (N) and species richness per grid cell (SR)
  4. Visualise N and SR patterns in Czech Republic

References

Any doubts?

https://github.com/petrkeil/Spatial-Ecology-and-Macroecology